Material and methods

To construct the map, we used the genotyping data of a population \(F_2\) consisted of 287 individuals, coming from the cross between Mimulus guttatus and Mimulus nasutus. As a result of the genotyping, 418 markers were obtained, of which 213 were codominant and 205 were dominant.
With the genotyping data, a genetic linkage map was constructed with software R (R CORE TEAM, 2018) and the “onemap” package (MARGARIDO et al., 2007).

data<-read_mapmaker(file = "m_feb06.raw")
##  --Read the following data:
##  Type of cross:          f2 
##  Number of individuals:  287 
##  Number of markers:      418 
##  Missing trait values:       
##    fl: 11 
##    fs: 19 
##    ft: 11 
##    ll: 20 
##    nv: 12 
##    pa: 35 
##   pal: 11 
##    pv: 12 
##    sa: 11 
##    sl: 11 
##    ss: 28 
##    tl: 11 
##    tp: 12 
##    tw: 11 
##    vi: 12 
##    ww: 11
class(data)
## [1] "onemap" "f2"
plot(data)

plot_by_segreg_type(data)

Segregation test

Initially, the markers was filter based in segregation distortion (3:1 dominant markers and 1:2:1 codominant markers). The \(\chi^2\) test was used for each marker at 5% significance, corrected for multiple tests based on Bonferroni correction.

segreg_test <- test_segregation(data)
print(segreg_test)
##        Marker    H0   Chi-square      p-value % genot.
## 1       AA461   3:1 9.601212e+00 1.944490e-03    95.82
## 2       AA420   3:1 8.836364e-01 3.472076e-01    95.82
## 3       AA404   3:1 1.843636e+00 1.745253e-01    95.82
## 4       AA384   3:1 3.938182e+00 4.720177e-02    95.82
## 5       AA378   3:1 1.236485e+01 4.374931e-04    95.82
## 6      AA371C 1:2:1 5.392727e+00 6.745034e-02    95.82
## 7       AA361   3:1 4.810909e+00 2.828012e-02    95.82
## 8       AA341   3:1 2.241212e+00 1.343756e-01    95.82
## 9       AA311   3:1 5.441212e+00 1.966702e-02    95.82
## 10      AA280   3:1 3.404848e+00 6.500508e-02    95.82
## 11      AA277   3:1 3.503030e-01 5.539416e-01    95.82
## 12      AA270   3:1 5.441212e+00 1.966702e-02    95.82
## 13      AA268   3:1 1.484848e+00 2.230175e-01    95.82
## 14      AA246   3:1 1.090909e-02 9.168149e-01    95.82
## 15      AA208   3:1 9.818182e-02 7.540225e-01    95.82
## 16     AA173C 1:2:1 1.892000e+01 7.790659e-05    95.82
## 17      AA167   3:1 2.048485e-01 6.508354e-01    95.82
## 18     AA166C 1:2:1 3.296703e-02 9.836516e-01    95.12
## 19      AA163   3:1 8.757576e+00 3.083186e-03    95.82
## 20      AA158   3:1 1.212121e-03 9.722268e-01    95.82
## 21      AA137   3:1 1.387758e+01 1.951126e-04    95.82
## 22      AA100   3:1 5.441212e+00 1.966702e-02    95.82
## 23       AA95   3:1 7.575758e-01 3.840882e-01    95.82
## 24       AA66   3:1 5.939394e-02 8.074564e-01    95.82
## 25      BA497   3:1 8.901099e-01 3.454475e-01    95.12
## 26      BA449   3:1 1.011111e+01 1.473781e-03    95.12
## 27      BA445   3:1 4.250305e+00 3.924328e-02    95.12
## 28      BA416   3:1 1.397924e+01 1.848400e-04    95.12
## 29      BA400   3:1 4.407814e-01 5.067455e-01    95.12
## 30      BA394   3:1 5.813187e+00 1.590644e-02    95.12
## 31      BA387   3:1 2.496825e+01 5.828210e-07    95.12
## 32      BA384   3:1 9.890110e-02 7.531524e-01    95.12
## 33      BA374   3:1 8.010989e+00 4.649434e-03    95.12
## 34      BA372   3:1 8.901099e-01 3.454475e-01    95.12
## 35      BA334   3:1 1.026862e+00 3.108968e-01    95.12
## 36      BA314   3:1 1.173382e+00 2.787074e-01    95.12
## 37      BA311   3:1 1.495726e+00 2.213301e-01    95.12
## 38      BA301   3:1 2.697192e+00 1.005252e-01    95.12
## 39      BA222   3:1 2.063492e-01 6.496440e-01    95.12
## 40      BA220   3:1 6.155067e+00 1.310361e-02    95.12
## 41      BA214   3:1 2.567155e+01 4.047501e-07    95.12
## 42      BA210   3:1 4.846154e+00 2.770785e-02    95.12
## 43      BA196   3:1 2.933455e+01 6.089999e-08    95.12
## 44      BA175   3:1 5.813187e+00 1.590644e-02    95.12
## 45      BA172   3:1 5.982906e-02 8.067663e-01    95.12
## 46      BA158   3:1 2.257631e+00 1.329573e-01    95.12
## 47      BA153   3:1 1.450672e+01 1.396608e-04    95.12
## 48      BA145   3:1 8.901099e-01 3.454475e-01    95.12
## 49      BA129   3:1 1.729060e+01 3.207700e-05    95.12
## 50      BA125   3:1 4.846154e+00 2.770785e-02    95.12
## 51      BA117   3:1 1.098901e-02 9.165119e-01    95.12
## 52      BA113   3:1 9.890110e-02 7.531524e-01    95.12
## 53       BA75   3:1 1.329670e+00 2.488639e-01    95.12
## 54       BA69   3:1 5.813187e+00 1.590644e-02    95.12
## 55      BB327   3:1 1.784652e+01 2.394564e-05    96.86
## 56      BB281   3:1 1.731415e+00 1.882303e-01    96.86
## 57      BB279   3:1 5.875300e+00 1.535476e-02    96.86
## 58      BB259   3:1 5.875300e+00 1.535476e-02    96.86
## 59      BB218   3:1 2.997602e+00 8.338786e-02    96.86
## 60      BB216   3:1 4.316547e-02 8.354140e-01    96.86
## 61      BB210   3:1 8.868106e+00 2.901961e-03    96.86
## 62      BB208   3:1 2.537170e+00 1.111939e-01    96.86
## 63      BB198   3:1 2.115108e+00 1.458518e-01    96.86
## 64      BB190   3:1 1.386091e+00 2.390663e-01    96.86
## 65      BB186   3:1 4.609113e+00 3.180248e-02    96.86
## 66      BB182   3:1 2.115108e+00 1.458518e-01    96.86
## 67      BB176   3:1 6.565947e+00 1.039484e-02    96.86
## 68      BB167   3:1 4.796163e-03 9.447872e-01    96.86
## 69      BB124   3:1 3.465228e+01 3.941770e-09    96.86
## 70      BB122   3:1 4.609113e+00 3.180248e-02    96.86
## 71      BB119   3:1 3.884892e-01 5.330946e-01    96.86
## 72      BB102   3:1 5.803357e-01 4.461808e-01    96.86
## 73      CA497   3:1 1.739130e-01 6.766573e-01    96.17
## 74      CA415   3:1 4.830918e-01 4.870252e-01    96.17
## 75      CA399   3:1 9.468599e-01 3.305199e-01    96.17
## 76      CA392   3:1 9.468599e-01 3.305199e-01    96.17
## 77      CA384   3:1 9.352657e+00 2.226624e-03    96.17
## 78      CA378   3:1 4.946860e+00 2.613810e-02    96.17
## 79      CA315   3:1 1.932367e+00 1.644997e-01    96.17
## 80      CA305   3:1 4.830918e-01 4.870252e-01    96.17
## 81      CA297   3:1 2.782609e+00 9.529284e-02    96.17
## 82      CA289   3:1 1.565217e+00 2.109029e-01    96.17
## 83      CA283   3:1 6.956522e-01 4.042485e-01    96.17
## 84      CA279   3:1 1.739130e-01 6.766573e-01    96.17
## 85      CA267   3:1 3.408696e+01 5.270336e-09    96.17
## 86      CA264   3:1 3.741063e+01 9.569921e-10    96.17
## 87      CA261   3:1 1.739130e-01 6.766573e-01    96.17
## 88      CA238   3:1 8.521739e+00 3.509290e-03    96.17
## 89      CA233   3:1 4.830918e-01 4.870252e-01    96.17
## 90      CA228   3:1 1.932367e-02 8.894426e-01    96.17
## 91      CA226   3:1 2.104348e+01 4.489784e-06    96.17
## 92      CA220   3:1 9.468599e-01 3.305199e-01    96.17
## 93      CA217   3:1 8.521739e+00 3.509290e-03    96.17
## 94      CA210   3:1 1.236715e+00 2.661051e-01    96.17
## 95      CA198   3:1 3.265700e+00 7.074280e-02    96.17
## 96      CA196   3:1 1.932367e-02 8.894426e-01    96.17
## 97      CA174   3:1 3.265700e+00 7.074280e-02    96.17
## 98      CA167   3:1 4.946860e+00 2.613810e-02    96.17
## 99     CA152C 1:2:1 1.239130e+00 5.381784e-01    96.17
## 100     CA150   3:1 1.207729e+01 5.103960e-04    96.17
## 101     CA140   3:1 2.338164e+00 1.262382e-01    96.17
## 102     CA131   3:1 1.932367e+00 1.644997e-01    96.17
## 103     CA122   3:1 0.000000e+00 1.000000e+00    96.17
## 104      CA96   3:1 3.265700e+00 7.074280e-02    96.17
## 105      CA75   3:1 6.956522e-01 4.042485e-01    96.17
## 106     CB333   3:1 1.083032e-02 9.171147e-01    96.52
## 107     CB329   3:1 1.474128e+00 2.246956e-01    96.52
## 108     CB309   3:1 4.188929e+00 4.068879e-02    96.52
## 109     CB280   3:1 3.008424e-02 8.622992e-01    96.52
## 110     CB272   3:1 2.707581e-01 6.028237e-01    96.52
## 111     CB257   3:1 1.156438e+00 2.822055e-01    96.52
## 112     CB246   3:1 2.033694e-01 6.520148e-01    96.52
## 113     CB230   3:1 1.227557e+01 4.589261e-04    96.52
## 114     CB216   3:1 3.477738e-01 5.553761e-01    96.52
## 115     CB187   3:1 3.008424e-02 8.622992e-01    96.52
## 116     CB173   3:1 4.477738e+00 3.433915e-02    96.52
## 117     CB172   3:1 6.412756e+00 1.133034e-02    96.52
## 118     CB166   3:1 3.477738e-01 5.553761e-01    96.52
## 119     CB162   3:1 1.012034e+00 3.144161e-01    96.52
## 120     CB156   3:1 2.889290e+00 8.917021e-02    96.52
## 121     CB126   3:1 1.456077e-01 7.027686e-01    96.52
## 122     CB115   3:1 7.510229e+00 6.134958e-03    96.52
## 123      CB55   3:1 1.179422e+01 5.941478e-04    96.52
## 124     BD433   3:1 9.157161e+00 2.477466e-03    91.64
## 125     BD429   3:1 2.799747e+00 9.427921e-02    91.64
## 126     BD411   3:1 4.575412e-01 4.987753e-01    91.64
## 127     BD371   3:1 2.130545e+00 1.443894e-01    91.64
## 128     BD340   3:1 3.619899e+01 1.781632e-09    91.64
## 129    BD316C 1:2:1 1.023846e+01 5.980622e-03    90.59
## 130     BD292   3:1 1.065906e+00 3.018720e-01    91.64
## 131     BD286   3:1 6.210393e-02 8.032010e-01    91.64
## 132     BD270   3:1 5.030418e+00 2.490588e-02    91.64
## 133     BD263   3:1 1.927757e+00 1.650041e-01    91.64
## 134     BD251   3:1 5.030418e+00 2.490588e-02    91.64
## 135     BD243   3:1 1.140684e-02 9.149454e-01    91.64
## 136     BD242   3:1 2.966920e+01 5.124252e-08    91.64
## 137     BD239   3:1 1.735108e+00 1.877599e-01    91.64
## 138     BD209   3:1 3.560203e+00 5.918051e-02    91.64
## 139     BD179   3:1 1.026616e-01 7.486587e-01    91.64
## 140     BD175   3:1 6.704689e-01 4.128882e-01    91.64
## 141     BD173   3:1 1.505830e+01 1.042408e-04    91.64
## 142     BD170   3:1 1.552598e+00 2.127523e-01    91.64
## 143     BD169   3:1 6.704689e-01 4.128882e-01    91.64
## 144     BD143   3:1 1.380228e+00 2.400623e-01    91.64
## 145     BD130   3:1 3.168568e-02 8.587193e-01    91.64
## 146     BD115   3:1 1.065906e+00 3.018720e-01    91.64
## 147     BD100   3:1 4.721039e+01 6.376146e-12    91.64
## 148      BD99   3:1 9.239544e-01 3.364388e-01    91.64
## 149      BD68   3:1 5.589354e-01 4.546895e-01    91.64
## 150      BD55   3:1 1.217997e+00 2.697540e-01    91.64
## 151    BD189C 1:2:1 1.503042e+01 5.447361e-04    91.64
## 152    AA118C 1:2:1 3.360364e+01 5.047346e-08    95.82
## 153    AA153C 1:2:1 3.938182e+00 1.395837e-01    95.82
## 154    AA296C 1:2:1 5.392727e+00 6.745034e-02    95.82
## 155    AA346C 1:2:1 5.162963e+00 7.566183e-02    94.08
## 156    AA374C 1:2:1 8.832117e-01 6.430030e-01    95.47
## 157    AA454C 1:2:1 1.780727e+01 1.358939e-04    95.82
## 158    BA245C 1:2:1 1.240659e+01 2.022751e-03    95.12
## 159    BA279C 1:2:1 2.708955e+00 2.580821e-01    93.38
## 160    BA396C 1:2:1 9.904412e+00 7.067801e-03    94.77
## 161    CA183C 1:2:1 1.355072e+00 5.078667e-01    96.17
## 162    CA258C 1:2:1 1.410870e+01 8.636458e-04    96.17
## 163    CA389C 1:2:1 2.791304e+01 8.684796e-07    96.17
## 164    CB263C 1:2:1 2.342960e+00 3.099079e-01    96.52
## 165    BB103C 1:2:1 3.851986e+00 1.457310e-01    96.52
## 166    AAT217 1:2:1 9.379845e-01 6.256324e-01    89.90
## 167    AAT225 1:2:1 3.435510e+01 3.466446e-08    85.37
## 168    AAT261 1:2:1 1.156432e+01 3.082058e-03    83.97
## 169    AAT267 1:2:1 7.976580e+01 4.776137e-18    93.73
## 170    AAT240 1:2:1 9.856115e-01 6.109099e-01    96.86
## 171    AAT278 1:2:1 4.620818e+00 9.922067e-02    93.73
## 172     AAT39 1:2:1 1.007168e+00 6.043606e-01    97.21
## 173    AAT211 1:2:1 1.966543e+00 3.740853e-01    93.73
## 174    AAT222 1:2:1 3.507246e+00 1.731455e-01    96.17
## 175    AAT374 1:2:1 1.404255e+00 4.955299e-01    98.26
## 176    AAT233 1:2:1 3.468000e+01 2.946685e-08    78.40
## 177    AAT265 1:2:1 8.398885e+01 5.781672e-19    93.73
## 178    AAT367 1:2:1 2.048052e+01 3.570357e-05    80.49
## 179    AAT372 1:2:1 3.870968e-01 8.240300e-01    86.41
## 180    AAT296 1:2:1 2.572016e+00 2.763718e-01    84.67
## 181    AAT230 1:2:1 2.436508e+00 2.957461e-01    87.80
## 182    AAT272 1:2:1 4.953933e+01 1.748526e-11    62.02
## 183    AAT308 1:2:1 1.687952e+01 2.161022e-04    86.76
## 184      AG19 1:2:1 7.138996e+00 2.816999e-02    90.24
## 185    AAT364 1:2:1 5.770492e+00 5.584106e-02    85.02
## 186    AAT300 1:2:1 1.692308e+00 4.290620e-01    72.47
## 187      CYCB 1:2:1 5.741036e+00 5.666957e-02    87.46
## 188    AAT242 1:2:1 1.776448e+01 1.388329e-04    90.24
## 189     BC546   3:1 8.354752e+00 3.846799e-03    86.76
## 190     BC542   3:1 3.481928e+00 6.204243e-02    86.76
## 191     BC512   3:1 4.832664e-01 4.869465e-01    86.76
## 192     BC506   3:1 3.868809e-01 5.339435e-01    86.76
## 193     BC498   3:1 1.457831e+00 2.272755e-01    86.76
## 194     BC478   3:1 7.133869e+00 7.564135e-03    86.76
## 195     BC392   3:1 8.783133e+00 3.040287e-03    86.76
## 196     BC388   3:1 1.649398e+01 4.880489e-05    86.76
## 197     BC379   3:1 6.559572e-02 7.978608e-01    86.76
## 198     BC376   3:1 3.012048e-01 5.831281e-01    86.76
## 199     BC374   3:1 6.559572e-02 7.978608e-01    86.76
## 200     BC334   3:1 4.659973e+00 3.087367e-02    86.76
## 201     BC330   3:1 7.937082e+00 4.843188e-03    86.76
## 202     BC321   3:1 2.710843e+00 9.966829e-02    86.76
## 203     BC266   3:1 9.222222e+00 2.390952e-03    86.76
## 204     BC243   3:1 4.349398e+00 3.702204e-02    86.76
## 205     BC219   3:1 2.957162e+00 8.549789e-02    86.76
## 206     BC216   3:1 1.108568e+01 8.699710e-04    86.76
## 207     BC199   3:1 3.012048e-01 5.831281e-01    86.76
## 208     BC192   3:1 1.312048e+01 2.920849e-04    86.76
## 209     BC167   3:1 3.346720e-02 8.548448e-01    86.76
## 210     BC135   3:1 2.250335e+00 1.335855e-01    86.76
## 211     BC131   3:1 1.084337e-01 7.419344e-01    86.76
## 212     BC126   3:1 3.481928e+00 6.204243e-02    86.76
## 213     BC125   3:1 1.204819e-02 9.125963e-01    86.76
## 214     BC108   3:1 3.760375e+00 5.248081e-02    86.76
## 215      BC83   3:1 1.084337e-01 7.419344e-01    86.76
## 216      BC80   3:1 9.222222e+00 2.390952e-03    86.76
## 217      BC70   3:1 3.868809e-01 5.339435e-01    86.76
## 218    BC586C 1:2:1 3.701613e+00 1.571104e-01    86.41
## 219    BC526C 1:2:1 1.961044e+01 5.516285e-05    86.76
## 220    BC194C 1:2:1 5.530120e+00 6.297231e-02    86.76
## 221    BC128C 1:2:1 1.478313e+01 6.164297e-04    86.76
## 222     CC540   3:1 4.878049e-02 8.251991e-01    85.71
## 223     CC531   3:1 4.878049e-02 8.251991e-01    85.71
## 224     CC457   3:1 9.159892e-01 3.385303e-01    85.71
## 225     CC450   3:1 2.655827e-01 6.063105e-01    85.71
## 226     CC447   3:1 6.639566e+00 9.973821e-03    85.71
## 227     CC402   3:1 3.387534e+00 6.569113e-02    85.71
## 228     CC392   3:1 2.655827e-01 6.063105e-01    85.71
## 229     CC387   3:1 3.387534e+00 6.569113e-02    85.71
## 230     CC381   3:1 9.159892e-01 3.385303e-01    85.71
## 231     CC378   3:1 5.420054e-03 9.413119e-01    85.71
## 232     CC371   3:1 1.355014e-01 7.127949e-01    85.71
## 233     CC359   3:1 1.355014e-01 7.127949e-01    85.71
## 234     CC342   3:1 2.289973e+01 1.706759e-06    85.71
## 235     CC330   3:1 3.951220e+00 4.683741e-02    85.71
## 236     CC320   3:1 2.016802e+01 7.092882e-06    85.71
## 237     CC286   3:1 5.902439e+00 1.511993e-02    85.71
## 238     CC283   3:1 5.902439e+00 1.511993e-02    85.71
## 239     CC270   3:1 1.097561e+01 9.231887e-04    85.71
## 240     CC262   3:1 2.867209e+00 9.040154e-02    85.71
## 241     CC150   3:1 9.159892e-01 3.385303e-01    85.71
## 242     CC149   3:1 4.390244e-01 5.075937e-01    85.71
## 243     CC138   3:1 5.420054e-03 9.413119e-01    85.71
## 244     CC132   3:1 2.655827e-01 6.063105e-01    85.71
## 245     CC130   3:1 4.878049e-02 8.251991e-01    85.71
## 246     CC126   3:1 2.655827e-01 6.063105e-01    85.71
## 247     CC124   3:1 9.159892e-01 3.385303e-01    85.71
## 248     CC114   3:1 5.902439e+00 1.511993e-02    85.71
## 249      CC93   3:1 6.639566e+00 9.973821e-03    85.71
## 250      CC61   3:1 5.902439e+00 1.511993e-02    85.71
## 251      CC53   3:1 2.016802e+01 7.092882e-06    85.71
## 252    CC385C 1:2:1 7.553719e+00 2.289448e-02    84.32
## 253    CC338C 1:2:1 1.253061e+00 5.344428e-01    85.37
## 254    CC171C 1:2:1 4.560976e+00 1.022343e-01    85.71
## 255    AAT312 1:2:1 5.761905e+00 5.608133e-02    58.54
## 256    AAT283 1:2:1 1.061176e+01 4.962318e-03    59.23
## 257       LFY 1:2:1 4.300000e+00 1.164842e-01    83.62
## 258    AAT333 1:2:1 1.211732e+01 2.337533e-03    62.37
## 259       AP3 1:2:1 1.550943e+01 4.287155e-04    73.87
## 260   MgSTS17 1:2:1 1.118182e+01 3.731634e-03    91.99
## 261   MgSTS16 1:2:1 4.877477e+01 2.562667e-11    77.35
## 262   MgSTS18 1:2:1 5.403101e+00 6.710140e-02    89.90
## 263   MgSTS20 1:2:1 2.630566e+01 1.939985e-06    92.33
## 264   MgSTS21 1:2:1 1.095726e+01 4.175035e-03    81.53
## 265   MgSTS19 1:2:1 3.225984e+01 9.882440e-08    88.50
## 266   MgSTS24 1:2:1 3.481890e+01 2.748985e-08    88.50
## 267   MgSTS25 1:2:1 3.996226e+00 1.355909e-01    92.33
## 268   MgSTS22 1:2:1 2.360000e+00 3.072787e-01    95.82
## 269   MgSTS27 1:2:1 8.687732e+00 1.298622e-02    93.73
## 270   MgSTS26 1:2:1 1.088764e+01 4.322937e-03    93.03
## 271   MgSTS23   3:1 4.473358e-01 5.036029e-01    93.73
## 272   MgSTS28 1:2:1 1.405714e+01 8.861969e-04    97.56
## 273  MgSTS105 1:2:1 1.745247e+00 4.178538e-01    91.64
## 274  MgSTS120 1:2:1 2.551471e+00 2.792256e-01    94.77
## 275   MgSTS29 1:2:1 3.222936e+01 1.003423e-07    75.96
## 276   MgSTS38 1:2:1 1.955253e+01 5.678351e-05    89.55
## 277   MgSTS91 1:2:1 1.871642e+01 8.625445e-05    93.38
## 278   MgSTS93 1:2:1 1.628571e+01 2.908051e-04    92.68
## 279  MgSTS133 1:2:1 1.422963e+01 8.129712e-04    94.08
## 280   MgSTS58 1:2:1 3.362264e+00 1.861631e-01    92.33
## 281   MgSTS55 1:2:1 2.533333e+00 2.817693e-01    94.08
## 282   MgSTS40 1:2:1 5.156134e+00 7.592062e-02    93.73
## 283   MgSTS98 1:2:1 6.773438e+00 3.381947e-02    89.20
## 284   MgSTS45 1:2:1 1.200000e+01 2.478752e-03    93.38
## 285   MgSTS11 1:2:1 1.066935e+01 4.821465e-03    86.41
## 286      CYCA 1:2:1 7.848815e+01 9.047205e-18    73.52
## 287    aat356 1:2:1 8.664255e+01 1.533941e-19    81.88
## 288   MgSTS87 1:2:1 1.025312e+02 5.440289e-23    89.20
## 289  MgSTS132 1:2:1 1.645161e+00 4.392965e-01    86.41
## 290  MgSTS212 1:2:1 2.655738e+00 2.650415e-01    85.02
## 291  MgSTS228 1:2:1 6.853846e+00 3.248675e-02    90.59
## 292  MgSTS229 1:2:1 3.383459e+00 1.842007e-01    92.68
## 293  MgSTS234 1:2:1 9.381356e+00 9.180460e-03    82.23
## 294  MgSTS245 1:2:1 2.538710e+01 3.070874e-06    86.41
## 295  MgSTS308 1:2:1 1.016736e+00 6.014763e-01    83.28
## 296  MgSTS316 1:2:1 8.869565e-01 6.418002e-01    80.14
## 297  MgSTS323 1:2:1 5.236364e+00 7.293535e-02    76.66
## 298   MgSTS36 1:2:1 8.737052e+00 1.266990e-02    87.46
## 299   MgSTS43 1:2:1 3.481013e+00 1.754316e-01    82.58
## 300  MgSTS437 1:2:1 1.066923e+01 4.821764e-03    90.59
## 301   MgSTS48 1:2:1 6.739496e+00 3.439831e-02    82.93
## 302   MgSTS49 1:2:1 3.825000e+00 1.477106e-01    83.62
## 303   MgSTS59 1:2:1 8.692308e+00 1.295655e-02    81.53
## 304   MgSTS68 1:2:1 2.275862e+00 3.204814e-01    80.84
## 305   MgSTS70 1:2:1 2.430120e+01 5.285188e-06    86.76
## 306  MgSTS508 1:2:1 9.843137e-01 6.113065e-01    88.85
## 307  MgSTS527 1:2:1 5.127344e+01 7.347076e-12    89.20
## 308  MgSTS520 1:2:1 2.141107e+01 2.242053e-05    88.15
## 309  MgSTS529 1:2:1 2.781250e+00 2.489197e-01    89.20
## 310  MgSTS455 1:2:1 1.584746e+00 4.527692e-01    82.23
## 311  MgSTS468 1:2:1 4.483607e+00 1.062667e-01    85.02
## 312  MgSTS480 1:2:1 1.167939e+00 5.576803e-01    91.29
## 313  MgSTS474 1:2:1 6.666667e-02 9.672161e-01    88.85
## 314  MgSTS113 1:2:1 5.995745e+00 4.989311e-02    81.88
## 315  MgSTS106 1:2:1 2.062992e+00 3.564733e-01    88.50
## 316   MgSTS69 1:2:1 1.144355e+01 3.273897e-03    86.41
## 317   MgSTS56 1:2:1 2.927419e+00 2.313763e-01    86.41
## 318   MgSTS31 1:2:1 1.204918e+00 5.474638e-01    85.02
## 319   MgSTS95 1:2:1 1.115242e-02 9.944393e-01    93.73
## 320  MgSTS360 1:2:1 5.600415e+01 6.900070e-13    83.97
## 321  MgSTS262 1:2:1 3.137615e+00 2.082935e-01    75.96
## 322   MgSTS50 1:2:1 2.857820e+00 2.395699e-01    73.52
## 323   MgSTS75 1:2:1 2.188152e+01 1.772103e-05    73.52
## 324   MgSTS76 1:2:1 1.277228e+00 5.280238e-01    70.38
## 325  MgSTS341 1:2:1 2.353476e+01 7.753396e-06    65.16
## 326  MgSTS388 1:2:1 2.078341e+00 3.537480e-01    75.61
## 327  MgSTS330 1:2:1 2.188841e-01 8.963341e-01    81.18
## 328  MgSTS336 1:2:1 2.081481e+01 3.020789e-05    56.45
## 329  MgSTS332 1:2:1 1.614451e+01 3.120790e-04    60.28
## 330  MgSTS326 1:2:1 2.165217e+00 3.387108e-01    80.14
## 331 MgSTS282B 1:2:1 6.225806e+00 4.447166e-02    86.41
## 332 MgSTS282A 1:2:1 4.364807e+00 1.127702e-01    81.18
## 333  MgSTS255 1:2:1 2.870968e+00 2.380002e-01    86.41
## 334  MgSTS350 1:2:1 3.967213e+00 1.375722e-01    85.02
## 335  MgSTS348 1:2:1 2.462400e+01 4.497450e-06    87.11
## 336  MgSTS362 1:2:1 3.388186e+00 1.837659e-01    82.58
## 337  MgSTS358 1:2:1 4.129365e+01 1.079438e-09    87.80
## 338  MgSTS344 1:2:1 5.963563e+00 5.070243e-02    86.06
## 339  MgSTS471 1:2:1 6.378689e+01 1.408815e-14    63.76
## 340   MgSTS37 1:2:1 1.902954e+00 3.861703e-01    82.58
## 341   MgSTS34 1:2:1 4.777778e+00 9.173155e-02    84.67
## 342  MgSTS426 1:2:1 5.252336e+00 7.235518e-02    74.56
## 343  MgSTS453 1:2:1 5.073469e+00 7.912434e-02    85.37
## 344  MgSTS456 1:2:1 9.271493e+00 9.698863e-03    77.00
## 345  MgSTS457 1:2:1 4.439462e-01 8.009369e-01    77.70
## 346  MgSTS491 1:2:1 2.559740e+01 2.764360e-06    80.49
## 347  MgSTS492 1:2:1 3.904348e+00 1.419651e-01    80.14
## 348  MgSTS513 1:2:1 1.430380e+00 4.890992e-01    82.58
## 349  MgSTS509 1:2:1 6.892562e+00 3.186392e-02    84.32
## 350  MgSTS500 1:2:1 1.457627e+00 4.824811e-01    82.23
## 351  MgSTS430 1:2:1 2.863415e+00 2.389007e-01    71.43
## 352  MgSTS381 1:2:1 1.452991e-01 9.299266e-01    81.53
## 353  MgSTS398 1:2:1 6.949524e+01 8.115229e-16    73.17
## 354  MgSTS314 1:2:1 0.000000e+00 1.000000e+00    80.84
## 355  MgSTS380 1:2:1 1.049244e+02 1.644230e-23    82.93
## 356  MgSTS251 1:2:1 3.894410e+00 1.426723e-01    56.10
## 357  MgSTS351 1:2:1 1.062385e+01 4.932415e-03    75.96
## 358  MgSTS347 1:2:1 1.651685e+00 4.378658e-01    93.03
## 359  MgSTS320 1:2:1 1.620710e+01 3.024634e-04    58.89
## 360  MgSTS293 1:2:1 2.828358e+00 2.431251e-01    93.38
## 361  MgSTS263 1:2:1 3.205419e+01 1.095271e-07    70.73
## 362  MgSTS578 1:2:1 6.134454e-01 7.358546e-01    82.93
## 363  MgSTS571 1:2:1 9.609375e-01 6.184934e-01    89.20
## 364 MgSTS574B 1:2:1 7.079681e+00 2.901795e-02    87.46
## 365 MgSTS574a 1:2:1 1.051613e+01 5.205370e-03    86.41
## 366  MgSTS579 1:2:1 1.838095e+00 3.988988e-01    73.17
## 367  MgSTS638 1:2:1 5.733333e+00 5.688824e-02    83.62
## 368  MgSTS590 1:2:1 8.326996e-01 6.594495e-01    91.64
## 369  MgSTS589 1:2:1 1.469636e+00 4.795928e-01    86.06
## 370  MgSTS583 1:2:1 3.979412e+01 2.284637e-09    94.77
## 371  MgSTS586 1:2:1 1.337008e+01 1.249466e-03    88.50
## 372  MgSTS535 1:2:1 2.205882e-02 9.890312e-01    94.77
## 373  MgSTS537 1:2:1 6.092308e+00 4.754142e-02    90.59
## 374  MgSTS538 1:2:1 2.595420e-01 8.782965e-01    91.29
## 375  MgSTS536 1:2:1 1.609665e+00 4.471627e-01    93.73
## 376  MgSTS539 1:2:1 4.567164e+00 1.019185e-01    93.38
## 377  MgSTS631 1:2:1 2.152399e+01 2.118976e-05    94.43
## 378  MgSTS563 1:2:1 5.462094e+00 6.515105e-02    96.52
## 379  MgSTS562 1:2:1 7.378161e+01 9.517593e-17    90.94
## 380  MgSTS561 1:2:1 9.463296e+01 2.823021e-21    93.03
## 381  MgSTS558 1:2:1 1.074820e+01 4.635085e-03    96.86
## 382  MgSTS548 1:2:1 1.852632e+01 9.485531e-05    79.44
## 383  MgSTS419 1:2:1 1.230769e-01 9.403168e-01    90.59
## 384  MgSTS611 1:2:1 1.416058e+00 4.926141e-01    95.47
## 385  MgSTS632 1:2:1 7.826087e-01 6.761743e-01    96.17
## 386  MgSTS609 1:2:1 1.564286e+00 4.574248e-01    97.56
## 387  MgSTS600 1:2:1 9.175182e+00 1.017734e-02    95.47
## 388  MgSTS565 1:2:1 1.378182e+00 5.020323e-01    95.82
## 389  MgSTS606 1:2:1 9.960000e+00 6.874063e-03    95.82
## 390  MgSTS577 1:2:1 1.300730e+01 1.497962e-03    95.47
## 391  MgSTS425 1:2:1 1.951095e+01 5.797640e-05    95.47
## 392  MgSTS438 1:2:1 8.078740e+00 1.760856e-02    88.50
## 393  MgSTS435 1:2:1 2.829801e+01 7.164147e-07    52.61
## 394  MgSTS494 1:2:1 1.079892e+02 3.551672e-24    97.21
## 395  MgSTS477 1:2:1 1.908425e+00 3.851153e-01    95.12
## 396  MgSTS483 1:2:1 6.404317e+01 1.239377e-14    96.86
## 397  MgSTS383 1:2:1 5.168498e+00 7.545272e-02    95.12
## 398 MgSTS504A 1:2:1 3.579926e+00 1.669664e-01    93.73
## 399 MgSTS504B 1:2:1 7.711111e+00 2.116184e-02    94.08
## 400 MgSTS504C 1:2:1 1.133333e+00 5.674137e-01    94.08
## 401  MgSTS545 1:2:1 1.298851e+00 5.223459e-01    90.94
## 402 MgSTS542A 1:2:1 2.238462e+00 3.265309e-01    90.59
## 403 MgSTS542B 1:2:1 1.249027e+00 5.355218e-01    89.55
## 404  MgSTS598 1:2:1 7.442623e+00 2.420221e-02    85.02
## 405  MgSTS441 1:2:1 5.146667e+00 7.628085e-02    52.26
## 406  MgSTS620 1:2:1 4.080916e+01 1.375319e-09    91.29
## 407  MgSTS104 1:2:1 7.349057e+00 2.536137e-02    73.87
## 408  MgSTS511 1:2:1 4.258427e+00 1.189308e-01    93.03
## 409  MgSTS621 1:2:1 2.014925e-01 9.041624e-01    93.38
## 410  MgSTS622 1:2:1 1.635294e+00 4.414692e-01    88.85
## 411  MgSTS459 1:2:1 3.283582e-01 8.485900e-01    93.38
## 412  MgSTS220 1:2:1 2.977695e+00 2.256325e-01    93.73
## 413  MgSTS214 1:2:1 1.342205e+00 5.111446e-01    91.64
## 414  MgSTS467 1:2:1 8.253219e+00 1.613750e-02    81.18
## 415  MgSTS470 1:2:1 1.096887e+01 4.150876e-03    89.55
## 416  MgSTS599 1:2:1 1.429644e+01 7.862613e-04    88.15
## 417  MgSTS431 1:2:1 7.651376e+00 2.180343e-02    75.96
## 418  MgSTS440 1:2:1 1.064516e+00 5.872774e-01    86.41
Bonferroni_alpha(segreg_test)
## [1] 0.0001196172
plot(segreg_test)

(no_dist<-select_segreg(segreg_test,distorted = F,numbers = T))
##   [1]   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  17  18
##  [18]  19  20  21  22  23  24  25  26  27  28  29  30  32  33  34  35  36
##  [35]  37  38  39  40  42  44  45  46  47  48  50  51  52  53  54  56  57
##  [52]  58  59  60  61  62  63  64  65  66  67  68  70  71  72  73  74  75
##  [69]  76  77  78  79  80  81  82  83  84  87  88  89  90  92  93  94  95
##  [86]  96  97  98  99 100 101 102 103 104 105 106 107 108 109 110 111 112
## [103] 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 129 130
## [120] 131 132 133 134 135 137 138 139 140 142 143 144 145 146 148 149 150
## [137] 151 153 154 155 156 157 158 159 160 161 162 164 165 166 168 170 171
## [154] 172 173 174 175 179 180 181 183 184 185 186 187 188 189 190 191 192
## [171] 193 194 195 197 198 199 200 201 202 203 204 205 206 207 208 209 210
## [188] 211 212 213 214 215 216 217 218 220 221 222 223 224 225 226 227 228
## [205] 229 230 231 232 233 235 237 238 239 240 241 242 243 244 245 246 247
## [222] 248 249 250 252 253 254 255 256 257 258 259 260 262 264 267 268 269
## [239] 270 271 272 273 274 278 279 280 281 282 283 284 285 289 290 291 292
## [256] 293 295 296 297 298 299 300 301 302 303 304 306 309 310 311 312 313
## [273] 314 315 316 317 318 319 321 322 324 326 327 329 330 331 332 333 334
## [290] 336 338 340 341 342 343 344 345 347 348 349 350 351 352 354 356 357
## [307] 358 359 360 362 363 364 365 366 367 368 369 371 372 373 374 375 376
## [324] 378 381 383 384 385 386 387 388 389 390 392 395 397 398 399 400 401
## [341] 402 403 404 405 407 408 409 410 411 412 413 414 415 416 417 418
(dist<-select_segreg(segreg_test,distorted = T,numbers = T))
##  [1]  16  31  41  43  49  55  69  85  86  91 128 136 141 147 152 163 167
## [18] 169 176 177 178 182 196 219 234 236 251 261 263 265 266 275 276 277
## [35] 286 287 288 294 305 307 308 320 323 325 328 335 337 339 346 353 355
## [52] 361 370 377 379 380 382 391 393 394 396 406

After filtering, 15% of markers with segregation distortion were identified. These markers were not used in the construction of the linkage map.

Grouping

The recombination fraction for all pairs of markers was estimated using the “rf_2pts” function. A sequence (“make_seq”) was created containing all markers that did not show segregation distortion. Then the markers were grouped using the “group” function based on the maximum recombination fraction of 0.3 and the maximum LOD calculated by the “suggest_lod” function (5.43).

twopts<-rf_2pts(data)
## Computing 87153 recombination fractions:
## 
##  0%  ........................................... 100%
mark <- make_seq(twopts, no_dist)
(LOD_sug <- suggest_lod(data))
## [1] 5.429707
LGs <- group(mark, LOD = LOD_sug, max.rf = 0.3)
##    Selecting markers: 
##    group    1 
##     .......
##    group    2 
##     ......................
##    group    3 
##     ............................................................
##     .......................
##    group    4 
##     .......................................
##    group    5 
##     ...............
##    group    6 
##     ...................................................
##    group    7 
##     ................................
##    group    8 
##     ..........................
##    group    9 
##     .............
##    group    10 
##     ......
##    group    11 
##     ........................
##    group    12 
##     .....................
##    group    13 
##     ......
##    group    14 
##     ...

Ordering

The clustering resulted in 14 linkage groups. We use the command “order_seq” to find the most likely order within each formed link group. The “doParallel” package was used to parallelize the process and optimize the analysis time.

cl<-makeCluster(detectCores()-1)
registerDoParallel(cl)

seq<-foreach (i = 1:LGs$n.groups,.packages = "onemap") %dopar% {
  assign("data",data,envir = .GlobalEnv)
  assign("twopts",twopts,envir = .GlobalEnv)
  make_seq(order_seq(input.seq= make_seq(LGs,i),twopt.alg ="rcd"), "force")
}
stopCluster(cl)
rm("cl")
plot<-list()
for (i in 1:LGs$n.groups){
  plot[[i]]<-rf_graph_table(seq[[i]],main = paste("Group",i),mrk.axis = "numbers")
}

Removing Markers

Markers that presented poor positioning in each group were removed based on the graphical analysis. These markers were excluded during the mapping process, using the “drop_mark” function.

plot[[1]]

plot[[2]]

rf_graph_table(map(drop_marker(seq[[2]],c(252,50,2,245,90,296,84))))

out_mark<-c(252,50,2,245,90,296,84)

plot[[3]]

rf_graph_table(map(drop_marker(seq[[3]],c(56,405,237,217,211,221,131,125,115,64,229,130,25,149))))

out_mark<-c(out_mark,56,405,237,217,211,221,131,125,115,64,229,130,25,149)

plot[[4]]

rf_graph_table(map(drop_marker(seq[[4]],c(4,293,111,239,126,77,146))))

out_mark<-c(out_mark,4,293,111,239,126,77,146)

plot[[5]]

rf_graph_table(map(drop_marker(seq[[5]],c(65))))

out_mark<-c(out_mark,65)

plot[[6]]

rf_graph_table(map(drop_marker(seq[[6]],c(181,20,246,6,204,312,213,150))))

out_mark<-c(out_mark,181,20,246,6,204,312,213,150)

plot[[7]]

plot[[8]]

rf_graph_table(map(drop_marker(seq[[8]],c(87,17,222,93))))

out_mark<-c(out_mark,87,17,222,93)

plot[[9]]

plot[[10]]

out_mark<-c(out_mark,seq[[10]]$seq.num)

plot[[11]]

rf_graph_table(map(drop_marker(seq[[11]],c(30,44))))

out_mark<-c(out_mark,30,44)

plot[[12]]

rf_graph_table(map(drop_marker(seq[[12]],c(117))))

out_mark<-c(out_mark,117)

plot[[13]]

plot[[14]]

After the markers were removed, the grouping and sorting were performed again. Fifteen groups were obtained and analyzed again, removing markers that presented a poor positioning from the linkage mapping. Group 15 was completely removed for presenting only 3 non-informative marks.

mark<-(no_dist)[!no_dist%in%out_mark]

mark <- make_seq(twopts, mark)
LGs <- group(mark, LOD = LOD_sug, max.rf = 0.3)
##    Selecting markers: 
##    group    1 
##     .......
##    group    2 
##     ..................
##    group    3 
##     ..............
##    group    4 
##     ...................
##    group    5 
##     ...........................................
##    group    6 
##     ................................
##    group    7 
##     ................................
##    group    8 
##     .............
##    group    9 
##     ................................
##    group    10 
##     ......................
##    group    11 
##     ....................
##    group    12 
##     ...............
##    group    13 
##     ......
##    group    14 
##     ......................
##    group    15 
##     ...
cl<-makeCluster(detectCores()-1)
registerDoParallel(cl)

seq<-foreach (i = 1:LGs$n.groups,.packages = "onemap") %dopar% {
  assign("data",data,envir = .GlobalEnv)
  assign("twopts",twopts,envir = .GlobalEnv)
  make_seq(order_seq(input.seq= make_seq(LGs,i),twopt.alg ="rcd"), "force")
}
stopCluster(cl)
rm("cl")
plot<-list()
for (i in 1:LGs$n.groups){
  plot[[i]]<-rf_graph_table(seq[[i]],main = paste("Group",i),mrk.axis = "numbers")
}

plot[[1]]

plot[[2]]

plot[[3]]

plot[[4]]

rf_graph_table(map(drop_marker(seq[[4]],c(116,71,168))))

seq[[4]]<-map(drop_marker(seq[[4]],c(116,71,168)))
out_mark<-c(out_mark,116,71,168)
plot[[5]]

rf_graph_table(map(drop_marker(seq[[5]],c(51,12))))

seq[[5]]<-map(drop_marker(seq[[5]],c(51,12)))
out_mark<-c(out_mark,51,12)

plot[[6]]

rf_graph_table(map(drop_marker(seq[[6]],c(46))))

seq[[6]]<-map(drop_marker(seq[[6]],c(46)))
out_mark<-c(out_mark,46)

plot[[7]]

rf_graph_table(map(drop_marker(seq[[7]],c(81,145))))

seq[[7]]<-map(drop_marker(seq[[7]],c(81,145)))
out_mark<-c(out_mark,81,145)

plot[[8]]

plot[[9]]

rf_graph_table(map(drop_marker(seq[[9]],c(256,108,408,329,124))))

seq[[9]]<-map(drop_marker(seq[[9]],c(256,108,408,329,124)))
out_mark<-c(out_mark,256,108,408,329,124)

plot[[10]]

plot[[11]]

plot[[12]]

plot[[13]]

plot[[14]]

rf_graph_table(map(drop_marker(seq[[14]],c(205,203,248,242))))

seq[[14]]<-map(drop_marker(seq[[14]],c(205,203,248,242)))
out_mark<-c(out_mark,205,203,248,242)

plot[[15]]

seq<-seq[-15]

draw_map2(seq[1:7],output = "m_feb06.jpeg",tag = "all",num = T,
          group.names = paste("Group",1:7),cex.label = .75)
## Completed
## Output file: /home/getulio/m_feb06/m_feb06(6).jpeg
draw_map2(seq[8:14],output = "m_feb06.jpeg",tag = "all",num = T,
          group.names = paste("Group",8:14),lim = 240,cex.label = .75)
## Completed
## Output file: /home/getulio/m_feb06/m_feb06(7).jpeg



##Literature Cited

Margarido G, de Souza A, Garcia A (2007). “OneMap: software for genetic mapping in outcrossing species.” Hereditas.

R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

Microsoft Corporation and Steve Weston (2018). doParallel: Foreach Parallel Adaptor for the ‘parallel’ Package.